Metroid: Alone
by Iccirrion
Summary: In the aftermath of the phazon crisis, the Galactic Federation have another job for Samus, simple recon on an uninhabited world beyond the borders of GF space. But danger of death isn't always what makes a difficult job. (Rated T for language and sexual references-Constructive Criticism is appreciated)
1. Prologue

**Prologue**

Samus stood quietly in the elevator as it ascended to the top of the Galactic Federation control tower. She looked out the window, it had been almost a month since she had last been on Norion, but for her, it was still too soon. Around every corner there were armed guards, every few feet on her way to the elevator she had passed an engineer, fixing broken plating or repairing the circuits to one system or another. She had been fighting the space pirates for years; she had even witnessed the complete destruction of an entire planet, two if Phaaze was considered a true planet. But she hadn't seen such destruction that had affected so many lives, Norion's defensive installations weren't the only areas attacked by the space pirates, even the civilian areas had suffered casualties. And it wasn't just Norion either, the Elysians, the sentient machines that watched over the Chozo's Skytown had lost their will against the phazon that had infected their planet, but even after the destruction of Phaaze, their systems had been so far corrupted that without the phazon powering their bodies, they simply failed, leaving the halls of Skytown empty.

The elevator shuddered as it arrived at the top of the tower, the doors opened revealing a room that had imprinted itself in Samus' mind, it was this room where she began one of her most difficult trials, her fight against the phazon corruption within her, even now she still suffered from muscle cramps and headaches that were allegedly caused by her body trying to readjust to normality.

"Samus, thank you for coming." The voice came from the centre of the room; Samus turned her gaze from the window to the circular table that had been installed in the centre of the room. Admiral Dane stood beside it and gestured for Samus to sit down. The Admiral was, as usual, in his full military dress, in all honesty Samus couldn't imagine him wearing anything else, he looked almost like he was the one designed for the uniform. Samus herself was as casual as she ever got when attending a briefing, her power suits helmet was offline and the large shoulders of the varia suit had been deactivated, she had even disabled the arm cannon that normally hid her right hand.

"So, what needs done this time?" Samus spoke quickly, in her mind a month's holiday wasn't enough after all she'd been through since her arrival at Tallon IV.

"Nothing too big." The Admiral responded, Samus sighed, she had thought the same thing during her initial briefing on the Olympus when she was told all she would have to do is upload a vaccine to couple of dozen supercomputers. "You may or may not know that when Phaaze was destroyed that existing phazon outside of the detonation range of the planet remained." The news mildly alarmed Samus, she had assumed that Phaaze was not only the source of phazon, but the object that sustained it. "That's not to say it was unaffected, phazon has since lost its limited sentience and virulent properties, but it has retained its high energy content and efficiency. This is why, with phazon now much safer to use, and in a very finite amount, the Galactic Federation has begun sourcing phazon from all sources we can find, including planets beyond our border, where we believe prototype leviathans were tested."

Samus listened carefully, she had thought she had beat the phazon problem after Tallorn IV and made the same mistake after defeating her doppelganger on Aether. Now that she knew that it wasn't all gone she didn't want to make any assumptions, no matter how many tests the GF had run.

"A week ago we sent a small fleet to HL-386 to begin phazon harvesting, since they arrived two days ago, we have had no word from them. We believe that the space pirates may have been involved." Samus nodded, it made perfect sense, the space pirates had been pushed back to their home world by the GF, if phazon was in a finite supply the space pirates only hope at retaliation would be to secure the majority of it for themselves. Which was just another reason for the GF to try and get it first. "Command considered sending a second fleet to the planet to investigate but we believe that we would just see a repeat of what's already happened. This is where you come in, we believe that a single small ship could sneak into the system and investigate, that is your mission. We need you to travel to HL-386, find out what happened to the fleet, gather intel on any possible hostile forces on the planet and extract survivors if necessary." Samus nodded and rose to her feet, no more information was needed, she would arrive at the planet, report what she found and return home. There was probably no need to extract anyone, if there really were space pirates there would be no survivors to extract, and if there weren't and it was just solar radiation or something of the like jamming communications, then extraction wouldn't be required. She turned and walked out of the room, on her way down in the elevator she reactivated her varia suit, helmet and arm cannon; she was on a mission now, even if it was a simple one, she had to take things seriously.

As Samus walked through the corridors, the marine's saluted and the engineers looked up from their work to give respectful nods. She smiled behind her green visor, for once a job seems to be paying off into something other than her credit stash. She soon arrived at the landing pad and entered her ship, before long the three landing struts lifted off the metal and the ship flow off. Within minutes of her leaving the control tower she was on her way towards the clouds, plotting a course to HL-386. Her computer flashed up a display: _**'5 Days/17 Hours/26 Minutes/43 Seconds'**_.

Samus began the stasis sequence and another 30 seconds was added onto the timer; the time required for the revival sequence. Samus lay back as her chair reclined and a field of blue and green energy began to wave in front of her face. Taking on last look at the displays around the ship and watching the light bend as her ship hit FTL, she took one final conscious breath before closing her eyes and losing herself to the artificial coma.


	2. Rude Awakening

**Chapter 1: Rude Awakening**

Samus woke with a start and instantly knew something was wrong, taking a second to glance around the cockpit confirmed that. Firstly, her skin was buzzing and her vision seemed even sharper than usual, which must've been caused by the ship's emergency revive, which solely consisted of several doses of pure adrenaline to wake Samus. Secondly, the arrival timer had stopped, albeit with only 27 seconds left, whatever caused the emergency revival had happened just seconds after she had dropped out of FTL, during the normal revival sequence. And last of all, a large, dark object was hurtling towards her ship.

Quickly activating the manual controls, Samus barely dodged the rubble as it flew over the top of the ship. Several warning lights flashed, indicating further obstacles. As Samus took a few seconds to survey her surroundings she saw that she had flown straight into a debris field, all around her were ruined ships, both Federation and Pirate. As she continued to dodge the wreckage the ships AI analysed the battlefield.

"_178 Individual wrecks identified: 3 Cruisers, 19 Frigates, 36 Transports and 120 Fighters. Alert: Galactic Federation logs indicate that the fleet sent to HL-386 included the Olympus-class Destroyer: GFS Pariah. No wreckage detected of the Pariah._" The voice spoke in its monotone drone. Samus tried looking herself for any wreckage, maybe there was something only eyes could see, but the AI seemed right, nothing looked like it once belonged to an Olympus-class.

"Commence a scan of the planet's surface, maybe they tried to land." Samus instructed, followed by a second of silence as the ship performed the task.

"_Alert: High levels of phazon on the HL-386's surface are distorting long-range readings._" Samus scowled, she would have to go down and commence a short-range scan.

"Begin preparations for landing." Samus ordered, followed almost instantly by the AI's droning reply.

"_Alert: the debris field has made it impossible to plot an automatic route to the planet, please begin manual operations._" Samus didn't complain, despite her annoyance, the AI was right; the debris would likely block any pre-programmed path. Placing her left hand on the ships navigation sphere she began guiding her ship slowly through the debris field. A ruined space pirate cruiser loomed into view, blocking the planet from Samus' sight; its three-pronged bow seemed to be reaching out for the sun. _'Even in ruins they can't stop reaching for glory._' Samus thought as she guided her ship between the prongs.

Just as she was about to clear the ship, an explosion tore through the ruined cruiser, rocking her own ship.

"_Alert: Space pirate cruiser does not appear entirely offline, self-destruction protocols have begun." _The AI alerted Samus, who was not at all amused that the AI hadn't detected that before she got this close. A shower of rubble crashed against the top of the ship as Samus quickly pulled away towards the planet, followed by a barrage of wreckage from the exploding ship. Scraps of metal and rock bounced off the ship and flew down with Samus towards the planet. Closing the blast shield over the window, Samus felt the ship warm up slightly before the AI readjusted the temperature as they entered the planet's atmosphere.

"_Alert: Ship hull integrity failing._" Another alert from the AI informed Samus again of something she had already known. Suddenly the ship shuddered, and Samus lurched forward, barely held back by the safety restraints. "_Alert: Multiple impacts have severely damaged primary engines, beginning preparation for emergency landing._" As soon as Samus heard the message she activated her gravity suit, if the ship was preparing to crash land, she would need as much protection as she could get.

It didn't take long before the ship impacted with the ground, its emergency thrusters desperately trying to slow the ship down. It bounced once before scraping along the ground, and coming to rest underneath a rocky outcropping.

Samus stood up from her chair inside the ship and deactivated her power suit completely. She gasped for air and swore, why, everywhere she went, did her ship end up getting disabled by inanimate objects.

"Ship, how long will the auto-repairs take?" Samus questioned, fearing the worst.

"_Moderate hull damage and major engine damage detected, ETA for repair completion: 39 hours._" Samus sighed, performing a scan now would just waste energy that needed to be spent, she would have to head out and manually survey the area. She took a step back to the platform in the centre of the ship and the hatch above her head opened as the floor rose up.

Samus had to duck as the lift reached the top of the ship, the rocky shelf the ship had landed under was lower than she had expected. Crawling along the top of the ship, she slid off the front, activating her power suit as she fell. She looked around at her temporary landing site.

She was in what seemed to be a crater of some sort, light streamed down from a cloudless sky, revealing several geemers crawling about on the roof and walls of the outcroppings. The ground was almost completely covered in a yellow-green fern and the occasional purple flower. Samus looked to her right and say a tunnel leading out of the crater. Deciding she had no better options she began walking, arm cannon raised, she had yet to find a planet where the creatures didn't try to kill her on sight.

About half an hour later, Samus was still walking, although her gun was lowered. At first she had been suspicious about the lack of dangerous life but later took it as it was, maybe she just had visited a poor choice of planets before.

Other than geemers the only other creatures she had seen were small flocks of birds that flew in and out of the caves around her. Her scan visor revealed nothing interesting other than that they seemed to have trace amounts of phazon in their bodies.

As she walked Samus arrived at an open room, there was a drop in front of her to a lower level, but from her current viewpoint she could see for miles around, including the Olympus-Class Destroyer that was impaled upon several large, thin spikes. She opened her scan visor, but both the Destroyer and the spikes were out of range, despite their size. She looked around and found similar structures in the room below her.

**Sharp rock formations are formed by a species of unidentified burrowers. The rock itself is an unknown alloy, although high concentrations of Malladium are detected within.**

Samus nodded to herself, it made sense that Malladium would be able to withstand even the impact of an Olympus-Class, although she wondered about what exactly that 'unidentified burrower' was, she had met several burrowing creatures in her life, many of them large, and almost all of them carnivorous. Taking a closer look at the ship she saw herself that there were several long scorch marks along its hull, most likely scars from the space pirate cruisers. Looking towards the rear of the ship, Samus noted that two of the three main engines seemed to be entirely destroyed, with the third still looking like it was in need of desperate repair. At least Samus had found the ship, and the likely cause of the crash, if the engines had been destroyed while in atmosphere landing a ship that size would have been impossible.

Suddenly the ships AI spoke up inside her helmet. "_Alert: Short range scanners within the varia suit have detected a Galactic Federation emergency beacon, updating map data._" Samus made a mental note to try and stop the AI saying 'Alert' every time it had something to say and opened her map. The beacon wasn't too far away, maybe another 15 minutes' walk. She dropped to the lower level, looked around once, and began to move on.

The journey was uneventful, with the lack of things trying to kill her Samus decided for once she would try and enjoy the rare moment of peace. She listened as the alien birds sung; the geemers chewed loudly on the thorns and even tried to enjoy the relaxing blue glow of the phazon pools she passed. She did have to agree with the GF, it really did seem like phazon was safer to use now, it was probably still radioactive but at least she couldn't feel the same...malevolence from it as she could before.

When Samus got closer to the beacon she noticed another cave entrance, the beacon was quite possibly through there. The cave branched off in both directions, a natural corridor almost perfectly perpendicular to the cave entrance. According to her map data, the beacon was to the right. Taking a quick look to the left to check for anything of interest, Samus entered the cave and started again towards the beacon. She had only taken a few steps before she was stopped by the all too familiar sound of a gun being leveled at her.

Samus jerked round, aiming her own weapon at the new threat, and paused. In front of her was a Federation marine, at least, she was. The grey power armour she wore was rusted in most places and covered in mud, at least the sections of it that didn't seem to have been removed. The visor had been completely removed revealing a determined face, covered in dirt and framed by several disheveled red hairs. The power suit seemed to be out of power, judging from the fact that all the normal blue lights on it were off, although Samus was fairly confident that the weapon the marine was holding was more than capable of firing.

The two stayed in place for several tense seconds, Samus knew that her armour could take a good few hits from a Federation rifle before failing, and in that time a quick power beam to the marine's unprotected face would end the battle instantly. Eventually the marine acted.

The rifle cluttered to the ground, Samus blinked, dropping a weapon was a very unusual response. The look of fierce determination had been wiped away, replaced by confusion. Seeing the threat as over Samus lowered her own weapon, the marine was obviously just frightened.

"Samus Aran?" The marine asked; it was obvious from her voice that this would not be the first question Samus would have to answer.

"Yes. Are you a crew-member of the Pariah?" Samus replied.

"Not anymore I guess. What are you doing here?" The marine replied. There was something else in her voice that Samus couldn't place, despite her extensive knowledge of human psychology it's much harder to utilize the knowledge in a Chozo classroom than on the field.

"I was sent by the Galactic Federation to assess the situation after contact was lost." Samus replied bluntly. "Are you the only survivor?"

"No clue, several escape pods were launched, but with the amount of phazon in this area and the presence of a space pirate encampment I'm not sure how many made it down." The marine removed her helmet, shaking her head to free her hair. Looking at the marine annoyed Samus, there was something familiar about her she just couldn't place.

Hooking her helmet under her left arm, the marine stood to attention and saluted, the old-fashioned way, a thumbs-up. This took Samus by surprise, she wasn't used to being saluted at all, and the thumbs-up hadn't been used in years.

"Why are..." before Samus could finish asking the marine smiled and turned her thumb to the ground. That further surprised Samus, only three people she knew well would ever give her that salute, and only one of them was a woman.

"Joanne?" Samus asked, even though she knew it couldn't be anyone else. Joanne smiled.

"Took you long enough." Joanne smiled as she walked up and punched Samus' shoulder.

Years ago, when Samus first joined the Galactic Federation army, she had shared a room with Joanne during their training. She had been one of the few other women joining the Marine Corps and one of the few people Samus had really talked to outside of her squad. Samus' wouldn't have called her a friend exactly, but both being young women, they were able to empathize with each other. Samus hadn't seen her since she was put under Adam's command and never bothered to try and get in contact again. They had met once since then, the day Samus left the Federation, they passed each other briefly in a corridor, greeted each other and went on their way.

"So, are you just here to survey or was evacuation part of your plan?" Joanne asked, "While I know enough to survive, shreikbat gets rather bland after a week."

"I did have instructions to evacuate survivors." Samus replied. Joanne frowned, something about Samus bothered her.

"Are we heading now, or are we going to look for others?" Joanne asked, still frowning.

"My ship took damage while entering the atmosphere; we won't be able to leave for a couple of days." Samus replied, her voice still blunt.

"Well then, I guess we should head to my camp, and you can take off the suit you know, there isn't anything really dangerous out here, I keep the route clear of shreikbats, and the geemers aren't aggressive." Joanne said. She didn't know what it was but something about Samus seemed off, this wasn't how she remembered her, and with that armor on it was impossible to tell body language or see her expression.

At first Samus was about to decline, but realised there wasn't any point, maintaining the power suit was something that was a drain on the mind when it wasn't actually being used, and Joanne's expression didn't show any signs of lying.

Samus' form glowed briefly and when it faded the armor was gone, replaced by her blue zero suit.

Joanne suppressed a scowl, Samus face was just as blank as her helmet and her pose only told her of the quiet confidence she already knew Samus had.

"Come on, I'll get us something to eat, and you can tell me the things about your adventures that aren't on the Federation's files."


	3. Change of heart

**Chapter 2: Change of heart**

Samus sat down in Joanne's makeshift camp, in a way she admired what the woman had done, the escape pod had been completely stripped down into anything useful, metal plates blocked all but one entrance, chair had been removed and converted into a bed and even one of the engine coils had been turned into a grill. That was something else Samus had to acknowledge, Joanne's skill as a hunter, several shriekbats were hung up on a cable that crosses the ceiling of the cave, all dead and with the acidic glands that caused them to explode carefully removed.

"So, phazon first appeared on Tallon IV, the Galactic Federation files say it was Aether it was first discovered." Joanne commented, Samus had also rediscovered Joanne's infinite curiosity; she didn't let anything go until she knew absolutely everything it knew. Samus had spent the last hour recalling her journey to Tallon IV, with several questions cropping up every few minutes.

"The Galactic Federation didn't discover phazon until after the incident of Aether, the Chozo on Tallon had been able to restrict the flow of phazon to within the impact crater of the prototype leviathan, so when the core detonated all the phazon was destroyed with it. When the Federation went in to clean up, there was nothing left for them to discover." Samus explained, her throat starting to hurt, she rarely took part in conversations, and talking for an hour straight was something she couldn't remember having any experience with.

Joanne nodded, throughout Samus' story she had been constantly analyzing her old friend for any emotional signs, but the bounty hunter's neutral face and stiff body language failed to give away anything.

"So, you have anything else you want to talk about?" She asked, maybe if she could get Samus to start talking herself something would come up. Samus sighed.

"You haven't changed at all, even when we did our training together you would force me to tell you all about how I felt during the exercise and what I thought of it. Aren't you ever satisfied with just what you know?" Samus said her voice still neutral, although Joanne did think she saw a flicker of a smile on her face.

"I already know everything I know, all that's left to learn is what other people know." Joanne said. "I wish I could say you haven't changed either, but you seem completely different." Deciding it might work to just tell her straight. "When did you become the ice queen you are now, what happened to that rebel always giving her superiors the thumbs down?"

Samus thought for a second, in her mind she hadn't changed, had she? She thought back to when she was in the Federation, when she had been so naïve, so driven by emotion, always fighting against the restraints placed upon her. She had relived that time not too long ago, on board the bottle ship, where Adam had sacrificed himself to destroy the metroids.

'_There_', Samus realized, the bottle ship had changed her, Adam's death made her swear to never again let herself be so influenced by emotion, if she had thought the situation through she would have seen the problem, she could have found a solution that didn't require Adam to die. She had learned that day, emotions are dangerous, they prevent logical thinking and impede progress, which in the end, costs lives.

Samus tried to think of an answer for Joanne, "In my line of work it pays to lack emotional connections." She thought back to just 6 months ago when she had killed Rhundas on Bryyo, back then she would have been killed if she had treated him as a friend, even if he had saved her life.

"That's no excuse, most people don't completely change their character just to fit into their job." Joanne retorted, Samus had still been hot-headed as ever when she left the Federation, so something must have happened after she had left. "I don't think even commander Malkovich would have been able to recognize who you are now." Samus' right arm twitched slightly at the mention of Adam, she didn't need Joanne bringing him into the conversation.

Joanne sighed, seeing a slight, if unidentifiable, change in Samus' expression. "It was commander Malkovich who got me my promotion you know, recommended me to the General. From there I actually managed to make commander myself. It was an interesting change, working with him rather than under him." Joanne spoke, trying to see if she could get anything else out of Samus, it did seem that she still had feelings for the old commander. "Then a couple of years ago he disappeared while he and his squad were investigating an illegal bio-weapon research center, no trace was ever found of the body. He was talking before he left about you, that he would have liked to see what you had done with yourself since…"

Joanne was suddenly interrupted as Samus slammed her fist against one of the metal barriers, her face displaying a clear emotion for the first time, anger. "You think I don't know what happened." Samus said through clenched teeth.

"How could you? The Bottle ship incident is highly confidential; I myself only got access to the files recently after my part in the assault on the space pirate Home world." Joanne said, puzzled by why Samus seemed so affected by even the mention of the incident.

Samus scoffed, '_Of course that's how it is, the Federation couldn't have some bounty hunter dealing with their problems, it must have been Adam's squad who dealt with the cloned Ridley and Metroid mother_'. "What your files probably forgot to mention is that I was on board the Bottle ship with Adam. I bet they also forgot to tell you that the Bottle ship was part funded by the Federation to propagate and militarize metroids." Samus said, her voice returning to its normal, calm tone. "I was the only one there who knows how Adam died." Her voice was slightly quieter as she mentioned Adam's death. "So don't try and explain to me about what you think happened on board that ship, I was there, I lived it."

Joanne paused for a second before straightening herself; she hadn't expected such an outburst from Samus, especially considering how composed she had been since she had arrived. "I'm sorry, the only listed survivor was listed as Anthony Higgs and he was sent back to Earth afterwards, the only source of information I had were the official documents." Joanne tried to explain as a silence fell over the pair. Joanne realized now; she had always seen, despite Samus' constant rebellion, that the two had been close, if Samus had been there with Adam as he died, no wonder she had changed, but Joanne still didn't like it.

Joanne opened her mouth to speak but decided against it. She just sat there, trying to think of how best to help her. Eventually she decided to speak up, "You'll have to get over it at some point Samus, even Adam wasn't this cold." Samus looked up at the mention of Adam's name.

"There's nothing to get over, this is who I am." Samus said bluntly. "I didn't come here for your counselling. If you want to talk about something you can start by explaining what happened since the fleet's arrival in the system."

Joanne sighed, "We arrived at HL-386 just over a week ago, as soon as we exited FTL we were attacked by a space pirate fleet already in orbit, they had just finished their own mining mission and were likely returning to whatever base they had come from, the fleet had a jamming ship that was likely why we didn't detect the fleet earlier and why we weren't able to contact the Federation. The Aurora unit on-board the Pariah was able to defend the fleet while the crew woke up but once we were in a full battle both sides started taking heavy casualties. We were fighting for about 4 hours before we managed to destroy two of the pirate cruisers and permanently disable the third, unfortunately our own communications array had been destroyed by the time we were able to destroy the jamming ship. The rest of the fleet had been destroyed, and our own engines were badly damaged so we decided to land on the surface to begin repairs, but on our way to the surface the damaged space pirate ship took several shots at our main engines, disabling them. At that point we were too close to the planet to pull out and the secondary thrusters weren't powerful enough to slow the ship down. I made my way to my squads assigned escape pod bay, before the rest of my squad could arrive however, the aurora unit went offline, sealing the blast doors. Before long the Pariah landed on the mountains to the north." Joanne bowed her head, "I left them behind, my squad. They'll all be dead by now." She fell silent, thinking back, she had to keep telling herself there was nothing she could've done. There were several long moments of silence.

"I'm going to go out and have a look around for any other pods." Samus said finally, standing up and walking out of the cave. Joanne remained silent.

* * *

><p>Once Samus was outside and found a flat plane she began running. She didn't have any intention of looking for pods, she just needed to get away from Joanne. '<em>What does she know about Adam.<em>' Samus thought to herself, still angry with herself for failing to suppress herself earlier. '_And who the hell does she think she is to tell me who I am._' A small voice in the back of her head tried to tell her that she didn't know who she was herself but she brutally repressed the thought.

Samus had been running for about half an hour when a voice suddenly called out.

"Freeze!"

Samus immediately rolled and drew her paralyser, searching for the owner of the voice. It didn't take too long. About a hundred metres away stood a human man in a black and grey jumpsuit, a Federation assault rifle on his right arm.

"Who are you, why are you here?" He called out, maintaining his distance and keeping his weapon trained on Samus.

Samus placed the paralyser back in its holster and stood up. "I'm Samus Aran. I'm here to investigate what happened to the phazon collection fleet." She answered.

The man straightened, lowered his weapon and started to walk towards Samus, his gaze slightly to the right so he wasn't looking directly at Samus.

"I'm Sergeant Hira of the Galactic Federation. I was onboard the Pariah when it was shot down by space pirates above..." He started explaining.

"I know what happened. Commander Brennen informed me of the ambush." Samus interrupted.

"Joanne's alive?" The sergeant asked to which Samus nodded, "I didn't think anyone else had been able to evade the pirate patrols. Thank god she's alright." A look of relief crossed the man's face. "Can you take me to her?"

Samus sighed, she had been hoping to run for a little longer. "Yes."

* * *

><p>Joanne sat on her makeshift bed examining the ring on her left hand, a gift from her fiancé from before they had began their tour with the promise that he would marry her as soon as the tour ended. She surprised herself again at how calm she was at his death, whenever she thought of her squad or friends onboard the Pariah she always got depressed but looking at her ring always made her smile. She wanted to think it was because it's not what he would have wanted but she wasn't sure, maybe she could sort herself out when she got back home.<p>

Joanne's thoughts trailed back to Samus as she lay back and gazed at the roof, she had decided again that she would try and appeal to Samus. She knew that talking about Adam had affected her, so she hadn't completely suppressed her emotions, but she wanted to avoid another outburst like before, so she would have to find something else to talk about. Maybe if Samus actually did find another survivor, then she could just talk and hopefully get Samus drawn in, it was hard to talk to someone on a one-to-one basis when they're a foot taller than you without an alien power suit.

Joanne sighed as she thought back to what Samus had been like in her Federation years, the short haired rebel. Always bending her orders and breaking regulations, it was only Adam's constant intervention that kept her from being dismissed. Even in battle Samus always seemed more fiery, the way she would always take the lead, bashfully entering unknown rooms, confident in her abilities and Chozo technology. Then upon returning to base she would always sit with Joanne over a meal as Joanne forced her to explain everything. Back then Samus laughed, she cried, she was a friend. Joanne sighed, it was doing no good thinking about the past, she had to focus on finding a way to return Samus to her old self, she thought. A tiny voice in her head told her that maybe it was best to leave Samus the way she was, people do change. Joanne sighed again, the voice was probably right, maybe she was still shocked from everyone around her who had died, she probably didn't want any more change.

Deciding not to think about it anymore, Joanne stood up and turned on her makeshift grill before reaching up and pulling a dead shriekbat down from the cable on the ceiling. They weren't exactly nice, but they were food. After a few seconds thought she pulled down another two, Samus would probably want to eat too, as would anyone she found. The coils on the repurposed engine started to glow orange as they heated, warming the room. "It's not all bad." Joanne told herself, "At least now you get to go home."


	4. Retaliation

**Chapter 3: Retaliation**

Joanne stood up as she heard footsteps approaching her cave, her gun in her hand.

"It's just me." Samus' voice called out from around the corner, Joanne sighed, she hadn't really expected space pirates but she could never be too careful. Soon enough Samus entered the cave, followed shortly by a tall, black-haired man. Joanne dropped her gun before running up and throwing her arms around him.

"Philip! You're alive." She said as she started sobbing into his shoulder. Philip responded by wrapping his own arms around her.

"So are you." He said, his voice a whisper.

Samus took a few steps back and sat down, Sergeant Hira had told her he was engaged to Joanne, she should have expected a scene like this. As the pair locked lips she turned her attention inward, analysing the status of her power suit, if only to serve as something to distract her. Samus found such displays of affection…awkward at best.

After about a minute Philip gently pushed Joanne away.

"You have another guest." He said gently, gesturing to Samus. "We shouldn't get too carried away."

"I know." Joanne said, despite the frown on her face, "I just thought I had dealt with it…you not being here anymore I mean."

Philip chuckled, "Am I that poor of a friend that you could forget me that quickly." Joanne punched his shoulder playfully.

"I didn't forget, I just didn't want to keep any attachments to ghosts." She said as she walked over to the makeshift grill, "I had just started cooking, if you don't mind shriekbat."

"So no-one else made it out alive?" Joanne asked as the three sat, carefully eating their meals.

"I wouldn't think so, most of my squad made it down, but the pirates from the encampment soon hunted them down." Philip sighed as he took another bite of his meal.

Samus had been ignoring the conversation between the two, of how they had managed to survive, preferring instead to focus on her food. She had never eaten shriekbat before, despite how often she encountered them, they tasted rather bland, like watered-down chicken, but it seemed nutritious enough, and Joanne had been eating them for a week and didn't seem to be displaying any side effects.

"Samus?" Philip asked, bringing Samus back to the conversation.

"Is there a problem?" she asked, as both he and Joanne set down their food.

"No problem, but we have a request to make." Philip said as he stood up, took a small piece of metal from the ground and walked over to one of the cave walls and began to draw a diagram. "While we appreciate that your job is to investigate what happened to the fleet and bring us back to Federation space, while evading space pirate patrols I have discovered their encampment." It was clear now his diagram was a map of the immediate area, he marked what Samus assumed to be their location with a cruder Federation logo, and another area with a claw shape, what must've been the space pirate encampment. "The encampment isn't too large, I would guess that there couldn't be more than forty, maybe fifty space pirates there. The problem is that they have a large quantity of phazon stored there, if they get a ship here before we do, the space pirates will gain a significant lead in terms of phazon." Philip had begun added in features surrounding the pirate encampment, tunnels, hills and other notable terrain. "We cannot allow the space pirates to secure that amount of phazon, so we need to take the encampment and either destroy the phazon or find another way to prevent the space pirates from securing it." Philip finished his map by adding a tunnel that connected the area around the encampment to a location Samus knew was not far from where they were. "The main problem is that Joanne and I are just two marines, with damaged gear and little ammunition, if we are to stand any chance of breaching the pirate defences, we will need you as a spearhead. Can you help us?" Philip asked finally.

Samus thought it over, of course she would help, she knew first-hand what the space pirates could do with their phazon powered weaponry. She analysed the map, if it was accurate there was a clear route right to their front door, she could always try sneaking around through one of the several side tunnels, but Samus wasn't really one for stealth in situations like this.

"I'll help, but we should move soon, I recommend at dawn, pirates are naturally nocturnal, if they're not expecting an assault they will have regular sleep patterns established, dawn will be when they are most tired, and easiest to fight." Samus explained. "We should go with a straight frontal assault, my power suit can provide the firepower we need to break through, I will need you two to act as eyes and ears, point out targets that you can't take care of yourself."

Philip and Joanne nodded, their minds back in the role of a soldier.

"If that's the case we should head to sleep ourselves." Philip spoke up, "No point striking when the enemy's tired if we're going to be tired ourselves."

"Agreed." Samus said as she stood up, "I will return to my ship, I will be back in the morning." And before waiting for a reply she left the cave.

"She's not like I imagined her." Philip said as Samus' footsteps couldn't be heard.

Joanne looked at the ground, "She definitely changed since I last saw her." She told him, "She said that she had seen Commander Malkovich die, it must have shaken her up badly." She shifted over beside him and planted a kiss on his cheek.

"We should get to sleep." Philip said, "We have to make sure we take this chance while we can. We can relax once we get back home."

As Samus approached her ship the sigil on the back of her left hand flashed once; a message from her ship. With a simple thought Samus activated the power suit, a quick command into her arm cannon bringing up the message.

"Repairs complete?" Samus asked as she read the message, "You told me that it would be over a day."

"_Repair time estimates were for average conditions. Actual conditions were at a near optimal level, moderate temperature, dry weather and lack of aggressive life forms had not been taken into account._" The monotone voice of the ship's AI spoke. Samus' would have been annoyed at the machine, but for once its information was good.

"Prepare for short term stasis and recovery, I want woken the instant the sun rises." Samus ordered the machine as she activated her ship command visor to guide the orange ship into the centre of the clearing, out from under the outcropping.

"_Stasis chamber ready. Daybreak in approximately 13 hours._" The AI spoke again as Samus entered the ship using the lower platform. She deactivated her suit and sat down in the command seat as it lowered into its flat state, a field of orange energy appearing around her as she closed her eyes.

Samus peeked around the corner, two space pirates stood guard at either side of the next doorway, the first they had met since setting out. They were standard troopers, their bodies showed signs of previous phazon corruption, but it was obvious they didn't have any phazon on them. Samus quickly turned the corner, firing a volley of shots at the one to her left, the last shot completely decapitating it. The second pirate tried to activate it's weapon as Joanne and Philip came around the corner, Joanne fired a quick burst, several shots finding their mark, killing the creature instantly. They stood for a few moments, waiting to see if the short fight had alerted any others.

Joanne yawned and stretched her arms up, receiving a glare from Samus.

"You had thirteen hours to sleep." Samus scolded, "How could you still be tired."

Joanne looked guiltily at the ground, "I might have taken it the wrong way when Philip asked me if I wanted to sleep with him."

Samus scowled, another reason to add to her list of why emotions were nothing but a hindrance. She really should have gone herself, it's not like she wasn't capable, she had all her equipment, if she had gone alone she could have just power bombed the place and been done with it.

Philip spoke up in the silence, "We should move on, we don't want to miss our chance."

Samus nodded, turning away from Joanne and carrying on down the tunnel.

"Remind me again why we have to do this at dawn, if they're nocturnal why don't we just attack at noon or something like that?" Joanne complained as they ran.

Philip answered before Samus had a chance to say anything, "Space pirates recover extremely quickly when asleep and they are easily woken, so if we wait until they're asleep they'll have recovered a fair bit."

Joanne nodded but kept silent; another pirate patrol had just appeared in front of them, a short, one-sided gunfight later they carried on through the tunnels.

Most of the journey was uneventful, a couple more patrols that needed eliminated, but mostly just running. Eventually they got to an opening in the tunnel, leading into a small courtyard that opened up to the sky, on the other side there was a large metal door, currently open, that led into a single large building.

"This must be the encampment." Joanne stated the obvious as they crept closer to the entrance.

"Watch for guards and alarms, their best soldiers are probably stationed here." Samus said as Philip stepped out of the cave. He looked around carefully as he slowly made his way across the courtyard, followed closely by Samus and Joanne.

Suddenly a siren went off inside the building, an invisible tripwire activated by Philip. The metal doors started to slide shut as several armoured space pirates entered the courtyard from the cave entrance.

"Go! I'll hold these ones off." Philip ordered as he turned and opened fire on the pirates. Joanne opened her mouth to complain, but as soon as the sound left her mouth Philip shouted back to her, "I can't let my commanding officer die, and we need Samus' firepower to destroy the encampment."

Samus grabbed Joanne's arm and dragged her inside the building, several more space pirates waited inside, although it was obvious these were the ones who had been preparing to rest, their movements were sluggish and few of their shots hit, Samus and Joanne quickly dispatched them as the door clunked shut behind them. Samus activated the booster on her suit and leaped up to the door control panel, and saw a problem.

A space pirate berserker had gotten into the courtyard, and it seemed smart enough to not use it's phazon based weaponry. She watched Philip dodge for a few seconds, she had to do something, without phazon weaponry of her own, she couldn't break through the armour on its back. Philip glanced up to Samus and quickly drew a finger across his throat. Samus got the message, Philip had noticed as well, that the courtyard was a pick-up point for phazon canisters. Inputting a quick command into the nearby console, Samus raised up several phazon canisters from the ground. She firing a shot at the window in front of her, shattering it, and began charging her arm cannon.

Back on the ground floor, Joanne was watching with despair as Philip was forced closer and closer into a corner by the berserker. The activated phazon canisters appearing scared her more, she looked up to see Samus aiming at one of the containers, her arm cannon glowing.

"Samus, don't, please!" Joanne pleaded as she realised what she was planning to do, "You can't just kill him."

On hearing Joanne's words, Samus hesitated, just long enough for her to say, "Soldiers die." Before releasing the blast of energy from her arm cannon.

The blast hit one of the canisters, instantly detonating the contents, causing a massive blue explosion to rip through the courtyard and the window Samus was standing at, knocking her back to the ground, several tanks of energy now depleted from her supply. Joanne collapsed to her knees, both the berserker and Philip had been completely engulfed by blue flame.

After about a minute the flames subsided, leaving behind the charred remains of the berserker and a blackened suit of Galactic Federation power armour, neither made a move.

Samus stood back up, she felt slightly ill, she couldn't say it was pleasant; killing another human being, but it had been necessary. The base had gone quiet, there mustn't have been as many space pirates in the base as they had thought, or they had already cannibalised some of their comrades.

Suddenly Samus felt an impact on her chest, a single unit of energy being lost from her suit's shielding, she looked down to see Joanne banging her fist against her, muffled sobs came from behind her helmet.

"You…Bitch." She tried to shout through her tears, "You killed him. You murderer." Samus stood there, watching her energy levels drop slowly before catching Joanne's fist in her free hand.

"There was no other choice." Samus explained, "If I hadn't detonated the phazon, all of us would have been killed."

Joanne stumbled back, "You should have tried to find a way, you could have saved him." She sobbed, slowly raising her rifle. "I thought we had been friends, I finally meet you again and you kill the man I love."

Samus reacted almost instinctively, quickly charging in and punching Joanne in the stomach, instantly knocking her out. As she laid her down on the ground, she signalled her ship to land in the courtyard. Her mission had been complete, the space pirate presence had been reduced enough to prevent further phazon mining, and she had rescued the lone survivor. She could head back, drop off Joanne on a medical frigate, give her briefing and move onto her next job. Maybe something that required more mindless shooting things, maybe those types of jobs were better for her, no having her emotions or ethics questioned.

As the ship landed and Samus carried Joanne out of the building, she stopped for a few moments before setting Joanne down and walking over to Philip's body. Removing his helmet revealed a face that didn't seem too badly damaged, he must have been killed by the impact of the explosion rather than the heat. Raising her left hand, Samus closed Philip's eyes before reaching down and removing his left gauntlet, she took the single gold ring from his finger and walked back over to Joanne, placing Philip's ring alongside her own, it was rather loose, but it would stay there for the journey. Samus briefly asked herself why she had done that, but couldn't find an answer, maybe she wasn't as rid of emotions as she had thought, maybe it was just her way of showing respect for Philip's sacrifice, either way, she had already done it, so decided to move on.

A few minutes passed before the orange ship took off and flew towards the morning sky, its destination already plotted, its occupants already in stasis. Leaving HL-386 far behind as its engines flared and it disappeared from sight.


	5. Epilogue

**Epilogue**

Samus sat on the main landing pad of Elysia's Skytown, her legs hanging off the edge. She liked it here, there was no human presence, and the watching the clouds swirling below helped her focus.

After arriving back at Norion, Samus had left a distraught Joanne off on an orbiting medical frigate. Samus hadn't been able to look her in the eye, despite everything, she did feel guilty for killing Philip. After arriving back at the control town on the surface, she had given Admiral Dane her debriefing, taken her payment, and immediately flew to Elysia.

She sighed, '_Is this really for the best?_' she asked herself as she sat there, '_Should I really leave everything to logic?_' The questions circled in her head, memories were resurfacing from her Galactic Federation days, her time with Adam, Anthony... and Joanne. Back then she had been able to laugh, smile, cry and love, had she given all that up just so she could become better at her chosen career.

Samus wondered about that as well; did she really want to live life as a bounty hunter? Did she have any choice, without her actions, who knows what the space pirates or Phaaze could have done to so many innocent people. '_Why was I given this power?_' Samus wondered to herself as she looked down at her armoured left hand, she had never really wanted the role of Galactic saviour but time and time again she found herself accepting the role.

A cargo drone buzzed over Samus' head, searching for its shipment, Samus looked up at it, such a simple life, picking things up, moving them somewhere else, getting routine maintenance. She shook her head, she shouldn't be thinking like that, she knew that she was still needed, the Space Pirates were still about, even with the loss of their homeworld, and soon enough the Federation would come asking for help again.

As Samus stood up her eyes wandered to the broken shell that had been the Leviathan that had plagued Elysia just six months ago. If she hadn't been around, the planet would've become another Phaaze, as would Bryyo and Norion. She had been the only one of the hunters able to overcome the Phazon corruption, no one else had been left to destroy the seeds.

She thought back to Joanne, she had mentioned fighting on Norion during the pirate attack, she would be dead too if Samus hadn't been there. Samus wondered, had Joanne thought of Samus still as a friend while fighting on Norion, or had she just been the mercenary recruited to help? Had she even realised that Samus had been on Norion before they met each other on HL-386? Samus knew she would never again be in the position where she could ask those questions, she only knew that now at any rate, she was no longer a friend of Joanne's.

A single, rebellious tear fell from Samus' left eye as she realised that with this, she really had lost all of her friends, Joanne had mentioned Anthony was still alive, but the last time Samus had met him, she had been addressed by her name, even he had moved on.

Samus tried to take strength in the fact she had just realized, she no longer had any ties in her mind, her family was dead, the race that raised her was extinct and she had no friends, there was nothing holding her back.

Samus let a few more tears fall before she turned back to her ship, she was free now, everything could be focused on her job, she didn't yet have a purpose, but others could give her one, she was a bounty hunter, the best, nothing more.

**Fin**

**Author notes.**

**-Thank you for reading Metroid:Alone. This story was mainly an experiment into writing a story about Samus that didn't revolve around action or a Galactic crisis. I wanted to quickly show my opinion of what I believe Samus is like under the suit. I have a plan for a story including Joanne that takes place after Fusion, but I'm uncertain of when I'll start that. Again, thank you for reading, if there was anything you liked, didn't like or have questions on leave a review or send me a PM, I very much appreciate any and all forms of feedback and will always try to get back to you.**

**-Iccirion**


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